Field of the Invention
The present invention describes compounds and methods useful as EBNA1 inhibitors, e.g., useful for the treatment of diseases caused by EBNA1 activity. The present invention also describes compounds and methods useful as EBNA1 inhibitors, e.g., useful for the treatment of diseases caused by the Epstein-Barr Virus (EBV).
Related Art
EBV is a human gamma-herpesvirus that infects over 90% of the adult population worldwide [Young, L. S. and A. B. Rickinson, Epstein-Barr virus: 40 years on, Nat. Rev. Cancer, 2004, 4:757-68; Rickinson, A. B. and E. Kieff, Epstein-Barr Virus, in Fields Virology, Third Edition, 1996, Lippincott-Raven Publishers, pp. 2397-446]. In combination with known and unknown cofactors, especially immunosuppression, EBV infection constitutes a high carcinogenic risk. EBV has been classified by the World Health Organization as a class I human carcinogen because of its causal association with Burkitt's lymphoma, nasopharyngeal carcinoma, ˜50% of all Hodgkin's lymphoma, gastric carcinoma, angiocentric T/NK lymphoma, and lymphoproliferative disorders of the immunosuppressed. It has been estimated that EBV is responsible for ˜1% of all human cancers worldwide [Parkin, D. M., F. Bray, J. Ferlay, and P. Pisani (2005) Global Cancer Statistics, 2002, Cancer J. Clin. 55:75-108]. The oncogenic potential of EBV is readily demonstrated in vitro by its capacity to immortalize primary B-lymphocytes in culture and in vivo by its ability to drive infected B-cells into aggressive lymphoblastic lymphomas in immunocompromised hosts.
EBV, like other herpesviruses, has a latent and lytic replication cycle. While the EBV lytic cycle is essential for viral transmission and increases risk of EBV-associated malignancy, it is the latent viral infection that is oncogenic [Thorley-Lawson, D. A. and A. Gross, Persistence of the Epstein-Barr virus and the origins of associated lymphomas, N. Engl. J. Med., 2004. 350:1328-37]. The latent virus expresses a limited set of viral genes that stimulate cellular proliferation and survival. Clinically available inhibitors of herpesvirus DNA polymerases, including variants of acyclovir (e.g. ganciclovir) and phosphonoacetic acid (e.g. foscarnet), have at least partial inhibitory activity against EBV lytic replication. However, none of the available herpesvirus antivirals are effective at blocking the virus from progressing to a latent infection or eliminating latent infection. Primary infections with EBV can evoke a robust, sometimes debilitating, immune response referred to as infectious mononucleosis (IM) [Vetsika, E. K. and M. Callan, Infectious mononucleosis and Epstein-Barr virus, Expert Rev. Mol. Med., 2004. 6:1-16]. Despite this robust immune reaction, the virus efficiently establishes latent infection in B-lymphocytes, where the virus can reside in long-lived memory B-cells [Babcock, G. J., L. L. Decker, M. Volk, and D. A. Thorley-Lawson, EBV persistence in memory B cells in vivo, Immunity, 1998, 9:395-404]. In some circumstances, latent infection can also be established in T-lymphocytes and epithelial cells. During latency, the virus does not produce infectious particles, and viral gene expression is limited to a subset of transcripts with growth-transforming and anti-apoptotic functions that contribute to EBV carcinogenesis. Thus, no existing anti-viral drug or immunological response can block the establishment of an EBV latent infection, which has the potential to drive lymphoid and epithelial cell oncogenic growth transformation.
Numerous studies have demonstrated that Epstein-Barr Nuclear Antigen 1 (EBNA1) is an ideal target for elimination of latent infection and treatment of EBV-associated disease. First, EBNA1 is expressed in all EBV-positive tumors [Leight, E. R. and B. Sugden, EBNA-1: a protein pivotal to latent infection by Epstein-Barr virus, Rev. Med. Virol., 2000, 10:83-100; Altmann, M., D. Pich, R. Ruiss, J. Wang, B. Sugden, and W. Hammerschmidt, Transcriptional activation by EBV nuclear antigen 1 is essential for the expression of EBV's transforming genes, Proc. Natl. Acad. Sci. USA, 2006, 103:14188-93]. Second, EBNA1 is required for immortalization of primary B-lymphocytes and for the stable maintenance of the EBV genome in latently infected cells [Humme, S., G. Reisbach, R. Feederle, H. J. Delecluse, K. Bousset, W. Hammerschmidt, and A. Schepers, The EBV nuclear antigen 1 (EBNA1) enhances B cell immortalization several thousand-fold, Proc. Natl. Acad. Sci. USA, 2003, 100:10989-94]. Third, genetic disruption of EBNA1 blocks the ability of EBV to immortalize primary human B-lymphocytes and causes loss of cell viability in previously established EBV-positive cell lines [Lee, M. A., M. E. Diamond, and J. L. Yates, Genetic evidence that EBNA-1 is needed for efficient, stable latent infection by Epstein-Barr virus, J. Virol., 1999. 73:2974-82]. Fourth, biochemical disruption of EBNA1 folding blocks the establishment of EBV latent infection. HSP90 inhibitors cause the selective killing of EBV+ B-cells and block lymphomagenesis in mouse models [Sun, X., E. A. Barlow, S. Ma S. R. Hagemeier, S. J. Duellman, R. R. Burgess, J. Tellam, R. Khanna, and S. C. Kenney, 2010, Hsp90 inhibitors block outgrowth of EBV-infected malignant cells in vitro and in vivo through an EBNA1-dependent mechanism, Proc. Natl. Acad. Sci. USA, 107:3146-51]. Fifth, EBNA1 is a noncellular viral oncoprotein that is functionally and structurally well characterized. The three-dimensional structure of EBNA1 bound to its cognate DNA sequence has been solved by X-ray crystallography [Bochkarev, A., J. A. Barwell, R. A. Pfuetzner, E. Bochkareva, L. Frappier, and A. M. Edwards, Crystal structure of the DNA-binding domain of the Epstein-Barr virus origin-binding protein, EBNA1, bound to DNA, Cell, 1996, 84:791-800; Bochkarev, A., J. A. Barwell, R. A. Pfuetzner, W. Furey, A. M. Edwards, and L. Frappier, Crystal structure of the DNA binding domain of the Epstein-Barr virus origin binding protein EBNA-1, Cell, 1995, 83:39-46; Bochkarev A, Bochkareva E, Frappier L, Edwards A M. The 2.2 Å structure of a permanganate-sensitive DNA site bound by the Epstein-Barr virus origin binding protein, EBNA1. J Mol Biol, 1998. 284:1273-78]. Analysis of the DNA binding domain reveals that EBNA1 protein is druggable, with several deep pockets and channels within the DNA binding domain that are predicted to disrupt DNA binding when bound to small molecules. Sixth, targeting a non-self viral-encoded protein for inhibition mitigates the potential risk of inherent toxicity. EBNA1 has a unique structural fold that is distinct from all known cellular DNA binding and replication proteins [Sun X, Barlow E A, Ma S, Hagemeier S R, Duellman S J, Burgess R R, Tellam J, Khanna R, Kenney S C. (2010) Hsp90 inhibitors block outgrowth of EBV-infected malignant cells in vitro and in vivo through an EBNA1-dependent mechanism. Proc Natl Acad Sci USA 107:3146-51; Bochkarev A, Barwell J A, Pfuetzner R A, Bochkareva E, Frappier L, Edwards A M. Crystal structure of the DNA-binding domain of the Epstein-Barr virus origin-binding protein, EBNA1, bound to DNA. Cell, 1996. 84:791-800; Bochkarev A, Barwell J A, Pfuetzner R A, Furey W, Edwards A M, Frappier L. Crystal structure of the DNA binding domain of the Epstein-Barr virus origin binding protein EBNA-1. Cell, 1995. 83:39-46]. Finally, the EBNA1 DNA binding function is essential for all known EBNA1 functions, including genome maintenance, DNA replication, transcription regulation, and host-cell survival [Leight, E. R. and B. Sugden, EBNA-1: a protein pivotal to latent infection by Epstein-Barr virus. Rev Med Virol, 2000. 10:83-100. Altmann M, Pich D, Ruiss R, Wang J, Sugden B, Hammerschmidt W. Transcriptional activation by EBV nuclear antigen 1 is essential for the expression of EBV's transforming genes. Proc Natl Acad Sci USA, 2006. 103:14188-93; Rawlins D R, Milman G, Hayward S D, Hayward G S. Sequence-specific DNA binding of the Epstein-Barr virus nuclear antigen (EBNA-1) to clustered sites in the plasmid maintenance region. Cell, 1985. 42:859-68; Ritzi M, Tillack K, Gerhardt J, Ott E, Humme S, Kremmer E, Hammerschmidt W, Schepers A. Complex protein-DNA dynamics at the latent origin of DNA replication of Epstein-Barr virus. J Cell Sci, 2003. 116:3971-84; Schepers A, Ritzi M, Bousset K, Kremmer E, Yates J L, Harwood J, Diffley J F, Hammerschmidt W. Human origin recognition complex binds to the region of the latent origin of DNA replication of Epstein-Barr virus. EMBO J, 2001. 20:4588-602]. Collectively, these studies demonstrate that EBNA1-DNA binding domain is an ideal and validated target for inhibition of EBV-latent infection and treatment of EBV-associated malignancies.
EBV plays a causative role in the tumorigenesis for a number of cancers including nasopharyngeal carcinoma, gastric carcinomas, non-hodgkin lymphoma (anaplastic large-cell lymphoma, angioimmunoblastic T-cell lymphoma, hepatosplenic T-cell lymphoma, B-cell lymphoma, Burkitt's lymphoma, reticuloendotheliosis, reticulosis, microglioma, diffuse large B-cell lymphoma, extranodal T/NK lymphoma/angiocentric lymphoma, follicular lymphoma, immunoblastic lymphoma, mucosa-associated lymphatic tissue lymphoma, B-cell chronic lymphocytic leukemia, mantle cell lymphoma, mediastinal large B cell lymphoma, lymphoplasmactic lymphoma, nodal marginal zone B cell lymphoma, splenic marginal zone lymphoma, intravascular large B-cell lymphoma, primary effusion lymphoma, lyphomatoid granulomatosis, angioimmunoblastic lymphadenopathy), leiomyosarcomas, X-linked lymphoproliferative disease, post-transplant lymphoproliferative disorders, Hodgkin's lymphoma and breast cancer. EBV has been classified as a class I human carcinogen responsible for at least 1% of all human cancer by the World Health Organization. EBV-associated malignancies account for more than 100,000 new cancer cases each year in the United States. An inhibitor of EBNA1 would change current clinical practice and be valuable for therapeutic treatment of EBV-associated diseases. Currently, nucleoside analogues (aciclovir, ganciclovir, foscarnet) can be used to treat lytic EBV infection and pathologies related to lytic EBV infection. However, these general anti-viral drugs are not specific for lytic EBV infection, and carry the risk of severe adverse effects. To date, no effective treatments exist for latent EBV infection, no treatment exists for pathologies related to latent EBV infection, and no treatments exist for the treatment of diseases associated with EBNA1.
EBV infection and EBNA1 have also been implicated in infectious mononucleosis [Henle W, Henle G. Epstein-Barr virus and infectious mononucleosis, N Engl J Med. 1973. 288:263-64; Vetsika E K, Callan M. Infectious mononucleosis and Epstein-Barr virus, Expert Rev Mol Med. 2004 6:1-16], chronic fatigue syndrome (CFS) [Watt T, Oberfoell S, Balise R, Lunn M R, Kar A K, Merrihew L, Bhangoo M S, Montoya J G. Response to valganciclovir in chronic fatigue syndrome patients with human herpesvirus 6 and Epstein-Barr virus IgG antibody titers. J Med Virol. 2012, 84:1967-74; Natelson B H, Ye N, Moul D E, Jenkins F J, Oren D A, Tapp W N, Cheng Y C. High titers of anti-Epstein-Barr virus DNA polymerase are found in patients with severe fatiguing illness. J Med Virol. 1994. 42:42-6; Wallace H L 2nd, Natelson B, Gause W, Hay J. Human herpesviruses in chronic fatigue syndrome. Clin Diagn Lab Immunol. 1999 6:216-23], multiple sclerosis [Tselis A. Epstein-Barr virus cause of multiple sclerosis, Curr Opin Rheumatol. 2012. 24:424-28; Lucas R M, Hughes A M, Lay M L, Ponsonby A L, Dwyer D E, Taylor B V, Pender M P. Epstein-Barr virus and multiple sclerosis, J Neurol Neurosurg Psychiatry. 2011. 82:1142-48; Ascherio A, Munger K L. Epstein-barr virus infection and multiple sclerosis: a review, J Neuroimmune Pharmacol. 2010. 3:271-77], systemic lupus erythematosus [Draborg A H, Duus K, Houen G. Epstein-Barr virus and systemic lupus erythematosus, Clin Dev Immunol. 2012: 370516; Doria A, Canova M, Tonon M, Zen M, Rampudda E, Bassi N, Atzeni F, Zampieri S, Ghirardello A. Infections as triggers and complications of systemic lupus erythematosus, Autoimmun Rev. 2008. 8:24-28; Poole B D, Scofield R H, Harley J B, James J A. Epstein-Barr virus and molecular mimicry in systemic lupus erythematosus. Autoimmunity. 2006 39:63-70], and rheumatoid arthritis [Lossius A, Johansen J N, Torkildsen Ø, Vartdal F, Holmøy T. Epstein-Barr virus in systemic lupus erythematosus, rheumatoid arthritis and multiple sclerosis—association and causation. Viruses. 2012. 4:3701-30; Balandraud N, Roudier J, Roudier C. Epstein-Barr virus and rheumatoid arthritis, Autoimmun Rev. 2004 3:362-67; Oliver J E, Silman A J. Risk factors for the development of rheumatoid arthritis. Scand J Rheumatol. 2006. 35:169-74]. Treatment with compounds that prevent EBV infection would provide therapeutic relief to patients suffering from infectious mononucleosis, multiple sclerosis, systemic lupus erythematosus, and rheumatoid arthritis. Further, treatment with compounds that prevent lytic EBV infection would provide therapeutic relief to patients suffering from infectious mononucleosis, multiple sclerosis, systemic lupus erythematosus, and rheumatoid arthritis. Further, treatment with compounds that prevent latent EBV infection would provide therapeutic relief to patients suffering from infectious mononucleosis, chronic fatigue syndrome, multiple sclerosis, systemic lupus erythematosus, and rheumatoid arthritis. Treatment with compounds that inhibit EBNA1 would provide therapeutic relief for suffering from infectious mononucleosis, chronic fatigue syndrome, multiple sclerosis, systemic lupus erythematosus, and rheumatoid arthritis. To date, however, no effective specific treatments exist for lytic EBV infection and no specific treatment exists for pathologies related to lytic EBV infection. In addition, to date, however, no effective treatments exist for latent EBV infection, no treatment exists for pathologies related to latent EBV infection, and no treatments exist for the treatment of diseases associated with EBNA1.
There is a long felt need for new treatments that are both disease-modifying and effective in treating patients that are refractory to current treatments for diseases and conditions associated with EBV infection such as nasopharyngeal carcinoma, gastric carcinomas, non-hodgkin lymphoma, anaplastic large-cell lymphoma, angioimmunoblastic T-cell lymphoma, hepatosplenic T-cell lymphoma, B-cell lymphoma, Burkitt's lymphoma, reticuloendotheliosis, reticulosis, microglioma, diffuse large B-cell lymphoma, extranodal T/NK lymphoma/angiocentric lymphoma, follicular lymphoma, immunoblastic lymphoma, mucosa-associated lymphatic tissue lymphoma, B-cell chronic lymphocytic leukemia, mantle cell lymphoma, mediastinal large B cell lymphoma, lymphoplasmactic lymphoma, nodal marginal zone B cell lymphoma, splenic marginal zone lymphoma, intravascular large B-cell lymphoma, primary effusion lymphoma, lyphomatoid granulomatosis, angioimmunoblastic lymphadenopathy, leiomyosarcomas, X-linked lymphoproliferative disease, post-transplant lymphoproliferative disorders, Hodgkin's lymphoma and breast cancer. There is also a long felt need for new treatments that are both disease-modifying and effective in treating patients that are refractory to current treatments for infectious mononucleosis. There is also a long felt need for new treatments that are both disease-modifying and effective in treating patients that are refractory to current treatments for chronic fatigues syndrome. There is also a long felt need for new treatments that are both disease-modifying and effective in treating patients that are refractory to current treatments for multiple sclerosis. There is also a long felt need for new treatments that are both disease-modifying and effective in treating patients that are refractory to current treatments for systemic lupus erythematosus. There is also a long felt need for new treatments that are both disease-modifying and effective in treating patients that are refractory to current treatments for rheumatoid arthritis. There is also a clear and present need for the treatment of EBV infection, and there is a long felt need for treatments that can specifically block lytic EBV infection. There is a long felt need for treatments that can block latent EBV infection. There is also a clear and present need for new treatments that are both disease-modifying and effective in treating diseases associated with EBNA1.
The present invention addresses the need to identify new treatments for diseases and conditions associated with EBV infection such as infectious mononucleosis, chronic fatigue syndrome, multiple sclerosis, systemic lupus erythematosus, and rheumatoid arthritis, and cancer, including nasopharyngeal carcinoma, gastric carcinomas, non-hodgkin lymphoma (anaplastic large-cell lymphoma, angioimmunoblastic T-cell lymphoma, hepatosplenic T-cell lymphoma, B-cell lymphoma, Burkitt's lymphoma, reticuloendotheliosis, reticulosis, microglioma, diffuse large B-cell lymphoma, extranodal T/NK lymphoma/angiocentric lymphoma, follicular lymphoma, immunoblastic lymphoma, mucosa-associated lymphatic tissue lymphoma, B-cell chronic lymphocytic leukemia, mantle cell lymphoma, mediastinal large B cell lymphoma, lymphoplasmactic lymphoma, nodal marginal zone B cell lymphoma, splenic marginal zone lymphoma, intravascular large B-cell lymphoma, primary effusion lymphoma, lyphomatoid granulomatosis, angioimmunoblastic lymphadenopathy), leiomyosarcomas, X-linked lymphoproliferative disease, post-transplant lymphoproliferative disorders, Hodgkin's lymphoma, and breast cancer by identifying novel EBNA1 inhibitors useful as therapeutic agents and in therapeutic compositions.